PDB-7n04: Crystal structure of the apo F240 antibody fragment

ID or keywords:

Entry

Database: PDB / ID: 7n04

Title

Crystal structure of the apo F240 antibody fragment

Components

Fab F240 heavy chain
Fab F240 light chain

Keywords

IMMUNE SYSTEM /

antibody /

Fab / anti-HIV /

gp41

Function / homology

alpha-D-glucopyranose

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.70000520394 Å

Authors

Cook, J.D. / Lee, J.E.

Funding support

Canada, 5items

Organization	Grant number	Country
Canadian Institutes of Health Research (CIHR)	MOP-115066	Canada
Canadian Institutes of Health Research (CIHR)	PJT-173301	Canada
Ontario Early Researcher Awards	ER-13-09-116	Canada
Canada Research Chairs	950-231672	Canada
Canada Foundation for Innovation		Canada

Citation

Journal: Commun Biol / Year: 2022
Title: Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies.
Authors: Cook, J.D. / Khondker, A. / Lee, J.E.

History

Deposition	May 25, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 30, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7n04.cif.gz	295.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7n04.ent.gz	218.6 KB	Display	PDB format
PDBx/mmJSON format	7n04.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/7n04 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/7n04	HTTPS FTP

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Related structure data

Related structure data	7n05C 7n07C 7n08C 1dfbS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #186 - Jun 2015 Receptor for Advanced Glycation End Products similarity (1)

Deposited unit

H: Fab F240 heavy chain

L: Fab F240 light chain

hetero molecules

51.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.996, 74.382, 145.041
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: Antibody

Fab F240 heavy chain

Mass: 26653.713 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HEK293T / Production host:

Homo sapiens (human)

#2: Antibody

Fab F240 light chain

Mass: 24363.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Cell line (production host): HEK293T / Production host:

Homo sapiens (human)

#3: Sugar

ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose /

Glucose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#4: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.49 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES-NaOH, pH 7.5, and 20% (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 4, 2014
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.7→44.71 Å / Num. obs: 54928 / % possible obs: 96.6 % / Redundancy: 2 % / B_iso Wilson estimate: 23.7901899698 Å² / CC_1/2: 1 / R_merge(I) obs: 0.023 / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.7→1.76 Å / R_merge(I) obs: 0.056 / Num. unique obs: 4303 / CC_1/2: 0.53 / % possible all: 76.7

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Processing

Software

Name	Version	Classification
PHENIX	1.10_2155	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb

Resolution: 1.70000520394→44.7076752723 Å / SU ML: 0.224743460608 / Cross valid method: THROUGHOUT / σ(F): 1.34454775085 / Phase error: 22.9834555405
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.221877027097	1998	3.63808517999 %
R_work	0.179349882926	52921	-
obs	0.180877855087	54919	96.5778598435 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 38.1791563834 Å²

Refinement step

Cycle: LAST / Resolution: 1.70000520394→44.7076752723 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3394	0	12	341	3747

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0101717588849	3505
X-RAY DIFFRACTION	f_angle_d	1.06362218998	4776
X-RAY DIFFRACTION	f_chiral_restr	0.0622099096331	541
X-RAY DIFFRACTION	f_plane_restr	0.00680947514659	610
X-RAY DIFFRACTION	f_dihedral_angle_d	14.3758118642	1267

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.70000520394-1.7425	0.39464991286	111	0.353556494514	2930	X-RAY DIFFRACTION	75.4403373853
1.7425-1.7896	0.362193146933	121	0.309046787515	3219	X-RAY DIFFRACTION	83.688298672
1.7896-1.8423	0.308305854741	135	0.268791050586	3560	X-RAY DIFFRACTION	92.8858722976
1.8423-1.9018	0.278481816211	146	0.23631145236	3872	X-RAY DIFFRACTION	99.7765085672
1.9018-1.9697	0.284472761377	145	0.228589679803	3857	X-RAY DIFFRACTION	99.8752183679
1.9697-2.0486	0.223166654183	146	0.174418212026	3880	X-RAY DIFFRACTION	99.9751676186
2.0486-2.1418	0.213433461752	148	0.177983051754	3881	X-RAY DIFFRACTION	99.95038452
2.1418-2.2547	0.232551976425	146	0.182564786328	3874	X-RAY DIFFRACTION	99.9751305645
2.2547-2.396	0.20201774822	147	0.175670041138	3899	X-RAY DIFFRACTION	99.9505928854
2.396-2.581	0.237800989882	146	0.17999481004	3901	X-RAY DIFFRACTION	100
2.581-2.8407	0.25084099298	149	0.180173424458	3935	X-RAY DIFFRACTION	99.9755201958
2.8407-3.2516	0.210013850509	150	0.175286461353	3950	X-RAY DIFFRACTION	100
3.2516-4.0963	0.194552433658	150	0.158425681166	3979	X-RAY DIFFRACTION	100
4.0963-44.7076	0.193384770967	158	0.156144098928	4184	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.91092814281	-2.47149993074	1.58782654842	5.07388020953	-2.01455040313	5.73884984062	0.0101002598943	-0.134187919173	-0.482842362692	0.0649331780048	0.210020161883	0.433103358475	0.129853707288	-0.367071195385	-0.36600015816	0.148536445154	0.0500413221988	0.058789390456	0.178552869804	0.0190698424716	0.189289847159	24.3609986668	43.6014435563	51.6249875229
2	3.22397996048	-0.561163120185	0.244046841952	2.35474631221	-0.486898188236	2.94101191806	-0.12720563205	-0.513038783243	-0.00211666471415	0.301782817514	0.140667637512	0.211012093226	-0.124117453952	-0.190121160552	-0.0353396917788	0.337044061815	0.1432011696	0.0764964238119	0.286698179162	0.022802699704	0.205722047891	28.1982091049	47.6958164352	60.4861901095
3	4.62793908721	-0.957709012672	2.1790425842	2.27602669352	-1.86270427312	2.05334240528	-0.148450093024	-0.770151746384	-0.21946019357	0.575572613568	0.198214499061	0.215623304152	-0.0807252544677	-0.0381643440528	0.295114317302	0.390868714351	0.154048213472	0.0769901608894	0.335621651381	0.0415940779583	0.180897337121	35.094116606	43.4264146777	62.2256459207
4	3.93887934238	-1.25233469038	0.042372490118	1.86593956183	-0.163807713231	5.25402633947	0.089842377302	-0.849202470065	0.178500170577	0.387612889117	0.171506549695	-0.212784421819	-0.378128007382	0.0665779867072	0.0489694539947	0.412515986995	0.138192762427	0.0616929864731	0.441408671672	0.0267555624796	0.221286201236	39.1685628331	44.3815507922	67.3744753486
5	0.470832346738	0.491567909812	-0.409256021869	0.515593910387	-0.167553315665	2.29835217495	-0.212772416619	0.0425368757425	0.0127419606965	0.385554550354	0.0740390822872	0.239368169766	-0.0500344807984	-0.205131067344	0.149429224866	0.194615396362	0.0754568151948	0.026778446565	0.220237965227	0.00542215521795	0.26153878165	24.3144395632	48.1840099935	40.9143653682
6	2.21286241078	-0.613445406092	-0.748803424074	3.14948231159	0.285821281217	2.81455707116	-0.0602661062606	0.124919144158	-0.0485903257818	-0.219178152513	0.0596963519257	-0.0927282644805	0.162547173288	-0.0534356713382	-0.00559001934859	0.0867248145568	-0.0232052437085	0.0116101960777	0.133792468734	-0.00789557477468	0.160790252229	32.2827396601	40.2087540766	25.4904373899
7	1.49385502619	0.990388818379	1.47883808513	2.10746012829	0.905553170688	1.74096725897	-0.0533887489114	0.294343568895	-0.193921952948	-0.382183011008	0.120525838873	0.118224283464	0.165088810522	-0.170416236139	0.473861746127	0.25260791668	-0.0568423609496	0.0534374300622	0.205315978133	0.0100319220898	0.234566024202	26.6949641284	33.8070275076	23.4000407237
8	0.739402021143	-0.655939647893	0.607639571795	1.65948847298	1.7513814344	8.68125010797	-0.0261415043148	0.561319692343	-0.305057084773	-0.5436731529	-0.00933303989281	0.376204001156	-0.403938996423	-0.121195019689	-0.101363509077	0.328671947701	-0.0722613785956	-0.0446655678936	0.396241051598	-0.0685243201905	0.285230569429	25.9000618462	37.2221525706	12.9410261602
9	5.01260753601	-3.58239519074	-3.40302001255	3.51511719847	3.26185576594	3.54061785405	-0.0398651127413	-0.016308096433	0.318823797574	0.300297566415	0.0661903909116	-0.442273373048	-0.364766009893	0.320649794347	-0.256620841903	0.292762154128	0.00323529434725	-0.0113981665458	0.201827755784	0.0200563585356	0.247120674887	55.8207450716	44.8778418551	49.5596727389
10	6.71525648764	5.39555805548	-4.17192657555	5.21117321559	-4.4855119856	4.23752151829	-0.127181262187	-0.688802600598	0.564121322204	0.604547675035	0.0437843053684	-0.200000756624	-1.07763817273	0.35013018459	-0.111318311325	0.5032205195	0.104354692437	-0.112784952278	0.348217066642	-0.133961198998	0.231143814759	53.2442791016	49.0483930134	71.071071085
11	4.89017357475	-0.247229764216	4.42106804966	1.55498492852	-1.03339968333	4.48756925719	0.0072982238883	0.0514317450357	-0.32239848624	0.115080958063	0.130345717485	0.11411199232	0.024786738099	-0.085288639294	-0.234287922033	0.228719617604	0.0711283918422	0.0190582874886	0.204519816207	-0.0184907467761	0.166989394418	44.4440202424	39.0172919342	53.7524772991
12	3.96659615782	-0.323009465119	-1.12254947338	4.43286234058	1.13334427369	4.91204572064	-0.28453793997	-0.329273497288	0.0275041631368	0.322036164567	0.184829263339	-0.184684563464	-0.122837124339	0.280894717152	0.107920610781	0.221103441312	0.0756850496622	-0.0608581034387	0.211139944573	0.00560554178786	0.18953198485	53.9582570426	38.1380588552	60.3448474249
13	1.35785764108	-0.392058938204	0.606798938153	1.26604402713	-0.907924123749	3.03260584701	0.0920982715392	0.0567940008094	0.160090198879	0.12645141507	-0.0448644449791	-0.303288242279	-0.181118682279	-0.0912865703456	-0.0578763342012	0.154437150397	0.056614935202	0.011206311608	0.165612136509	-0.00320542271706	0.187308430811	49.4582199835	42.4709815099	49.4595790751
14	2.26224274957	1.5280600301	0.902285355882	2.19341733782	-0.438041685185	4.89534204792	-0.0256956448681	0.622427628715	-0.0197409524826	-0.412686721991	0.1072514618	0.426086641723	0.348568212723	-0.466713714057	-0.188688384289	0.148825926173	-0.0549443531679	-0.0302506579958	0.273424137263	0.0115040952106	0.222348123289	32.4962427895	46.6230492783	15.0122482677
15	4.61450475482	-4.49777195875	4.49773316787	6.18001285352	-4.44435029356	5.38121683827	-0.234072459376	-0.173466248239	0.0968289834961	-0.0405480669605	0.00242637049443	-0.311387996494	-0.0370911905263	0.268087054609	0.226269200141	0.0857424644745	0.0067412748145	0.0544374834021	0.192078270018	-0.0175109418648	0.127210086945	45.1739495176	48.0023750028	23.452956824
16	1.54961608455	0.546736082808	0.0601942168835	9.08680484775	-6.23678765267	4.41881755284	-0.0285312500205	0.0343142334304	0.208186695622	-0.14738333835	-0.0131533367465	0.024974634844	-0.15584587277	0.359333315658	0.175333985768	0.239961169359	-0.0434810789337	0.00843121750967	0.21425389134	-0.0229256143036	0.274451134647	41.6453724924	56.4768836728	21.7177158868
17	3.51940164677	-2.63220966899	3.25129509427	4.41891321628	-4.36915556165	7.83467554231	-0.0696140798821	-0.023687291019	-0.0302588494287	-0.231901225157	0.171221057872	0.114032443278	0.0646670961401	0.0469514883639	-0.0786673220552	0.109524482901	-0.031409362582	0.011467097694	0.105656984697	-0.0321213706094	0.153499956709	40.9248466026	48.6008987158	21.2874446224
18	7.95607470671	-2.41556707558	3.84500131345	3.94797600125	-1.69170839977	4.7018564738	0.00473385414148	0.453871494564	0.164801237643	-0.685381734803	-0.326515733671	-0.253537167924	0.0872682482475	1.20630709798	-0.261585478313	0.0792524297552	0.00999000202	0.140231704916	0.421819681499	0.0300782427662	0.151461083754	48.3038138419	48.0739474257	14.3226351324

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'H' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'H' and (resid 18 through 87 )
3	X-RAY DIFFRACTION	3	chain 'H' and (resid 88 through 99 )
4	X-RAY DIFFRACTION	4	chain 'H' and (resid 100 through 103 )
5	X-RAY DIFFRACTION	5	chain 'H' and (resid 104 through 119 )
6	X-RAY DIFFRACTION	6	chain 'H' and (resid 120 through 188 )
7	X-RAY DIFFRACTION	7	chain 'H' and (resid 189 through 203 )
8	X-RAY DIFFRACTION	8	chain 'H' and (resid 204 through 220 )
9	X-RAY DIFFRACTION	9	chain 'L' and (resid 3 through 25 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 26 through 32 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 33 through 48 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 49 through 75 )
13	X-RAY DIFFRACTION	13	chain 'L' and (resid 76 through 113 )
14	X-RAY DIFFRACTION	14	chain 'L' and (resid 114 through 128 )
15	X-RAY DIFFRACTION	15	chain 'L' and (resid 129 through 150 )
16	X-RAY DIFFRACTION	16	chain 'L' and (resid 151 through 163 )
17	X-RAY DIFFRACTION	17	chain 'L' and (resid 164 through 197 )
18	X-RAY DIFFRACTION	18	chain 'L' and (resid 198 through 213 )

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